cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf Paramecium-biaurelia-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-biaurelia-GSF869-Doak-Ugne-223_S10-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf Paramecium-biaurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-biaurelia-GSF869-Doak-Ugne-NiA_S11-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf Paramecium-biaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-biaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf Paramecium_primaurelia-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes sam_reads_genes-Paramecium_primaurelia-GSF869-Doak-Ugne-223_S10-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf Paramecium_primaurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes sam_reads_genes-Paramecium_primaurelia-GSF869-Doak-Ugne-227_S13-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf Paramecium_primaurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes sam_reads_genes-Paramecium_primaurelia-GSF869-Doak-Ugne-NiA_S11-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf Paramecium_primaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes sam_reads_genes-Paramecium_primaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf Paramecium-sexaurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-sexaurelia-GSF869-Doak-Ugne-227_S13-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf Paramecium-sexaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-sexaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.chrom.sizes sam_reads_genes-Paramecium_tetraurelia-GSF869-Doak-Ugne-209_S7-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.chrom.sizes sam_reads_genes-Paramecium_tetraurelia-GSF869-Doak-Ugne-223_S10-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.chrom.sizes sam_reads_genes-Paramecium_tetraurelia-GSF869-Doak-Ugne-227_S13-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia-GSF869-Doak-Ugne-328_S12-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.chrom.sizes sam_reads_genes-Paramecium_tetraurelia-GSF869-Doak-Ugne-328_S12-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.chrom.sizes sam_reads_genes-Paramecium_tetraurelia-GSF869-Doak-Ugne-NiA_S11-2x100 -nomulti